mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 4,604,344 | 0 | C | T | 44.6% | 46.0 / 53.8 | 65 | S62F (TCT→TTT) | bglJ | DNA‑binding transcriptional regulator BglJ |
| * | NC_000913 | 3,206,435 | 0 | C | T | 34.4% | 35.3 / 18.9 | 32 | intergenic (‑179/‑28) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 753,125 | 0 | T | A | 33.3% | 90.1 / 29.5 | 54 | intergenic (‑330/+60) | ybgD/gltA | putative fimbrial protein YbgD/citrate synthase |
| * | NC_000913 | 1,550,663 | 0 | A | C | 32.0% | 82.3 / 20.8 | 50 | N68T (AAC→ACC) | fdnH | formate dehydrogenase N subunit beta |
| * | NC_000913 | 3,206,444 | 0 | T | A | 30.3% | 45.7 / 12.2 | 33 | intergenic (‑188/‑19) | ttdR/ttdA | DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha |
| * | NC_000913 | 650,809 | 0 | T | G | 29.2% | 92.6 / 11.5 | 48 | T350P (ACC→CCC) | citC | citrate lyase synthetase |
| * | NC_000913 | 4,568,504 | 0 | T | G | 28.7% | 168.4 / 15.8 | 88 | T6P (ACC→CCC) | mdtM | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| * | NC_000913 | 3,556,207 | 0 | T | C | 25.0% | 76.5 / 10.1 | 40 | S215G (AGT→GGT) | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | NC_000913 | 2,326,450 | 0 | T | G | 23.4% | 125.8 / 33.0 | 64 | G114G (GGT→GGG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 1,435,727 | 0 | G | A | 23.3% | 93.0 / 16.1 | 43 | intergenic (‑108/+33) | uspF/ompN | nucleotide binding filament protein/outer membrane porin N |
| * | NC_000913 | 2,236,876 | 0 | A | C | 22.4% | 123.9 / 16.2 | 58 | V293G (GTA→GGA) | mglC | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| * | NC_000913 | 4,447,434 | 0 | C | A | 22.0% | 293.5 / 54.4 | 100 | P1108Q (CCG→CAG) | tamB | translocation and assembly module subunit TamB |
| * | NC_000913 | 4,101,514 | 0 | G | T | 21.4% | 159.6 / 17.5 | 57 | intergenic (+84/‑176) | sodA/kdgT | superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| * | NC_000913 | 4,296,060 | 0 | C | T | 21.2% | 175.7 / 40.2 | 80 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 445,558 | 0 | A | C | 21.1% | 79.6 / 13.1 | 38 | V370G (GTA→GGA) | yajR | putative major facilitator superfamily transport protein YajR |
| * | NC_000913 | 3,240,985 | 0 | T | G | 21.0% | 144.8 / 11.2 | 63 | S348A (TCT→GCT) | sstT | serine/threonine:Na(+) symporter |
| * | NC_000913 | 4,213,051 | 0 | A | C | 20.0% | 34.4 / 10.1 | 20 | noncoding (12/120 nt) | rrfE | 5S ribosomal RNA |
| Marginal new junction evidence (lowest skew 10 of 17 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 43 (0.530) | 15 (0.200) | 14/258 | 3.6 | 23.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 58 (0.760) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 10 (0.180) | 8/190 | 4.0 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 6 (0.090) | 4/224 | 6.4 | 7.8% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 71 (1.070) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 6 (0.070) +T |
5/274 | 6.8 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | = 3424783 | 1 (0.010) | 4 (0.050) +GG |
4/264 | 7.1 | 35.1% | noncoding (2001/2904 nt) | rrlD | 23S ribosomal RNA |
| ? | NC_000913 | = 4039514 | 14 (0.170) | noncoding (1996/2905 nt) | rrlA | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3424783 | 1 (0.010) | 4 (0.050) +GG |
4/264 | 7.1 | 57.5% | noncoding (2001/2904 nt) | rrlD | 23S ribosomal RNA |
| ? | NC_000913 | = 3945698 | 5 (0.060) | noncoding (1995/2904 nt) | rrlC | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | 3139623 = | NA (NA) | 3 (0.040) | 3/234 | 7.1 | NA | noncoding (33/34 nt) | other | REP221a |
| ? | NC_000913 | 3150742 = | NA (NA) | noncoding (32/34 nt) | other | REP222d | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 6 (0.080) | 4/260 | 7.1 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 4039516 | 10 (0.120) | 4 (0.050) | 4/272 | 7.3 | 28.9% | noncoding (1998/2905 nt) | rrlA | 23S ribosomal RNA |
| ? | NC_000913 | 4039520 = | NA (NA) | noncoding (2002/2905 nt) | rrlA | 23S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3945700 | NA (NA) | 4 (0.050) | 4/272 | 7.3 | NA | noncoding (1997/2904 nt) | rrlC | 23S ribosomal RNA |
| ? | NC_000913 | 3945704 = | NA (NA) | noncoding (2001/2904 nt) | rrlC | 23S ribosomal RNA | |||||